Cyber-Physical Systems (CPS) play a vital role in modern smart environments like smart grids, healthcare systems, industrial automation, and intelligent transport systems. Ensuring secure and efficient communication in CPS is challenging due to rising cyber threats and data privacy issues. Traditional cryptographic techniques are becoming insufficient, especially with the growing threat of quantum computing. This research proposes a security framework for improving throughput efficiency of cyber-physical systems communications using quantum cryptography by implementing the B92 Quantum Key Distribution (QKD) protocol. The B92 protocol utilizes only two non-orthogonal quantum vectors for secure key generation and distribution, reducing resource consumption and communication overhead. The proposed framework is simulated using MATLAB to model CPS secure communication and evaluate performance metrics such as throughput efficiency, key production rate, quantum bit error rate (QBER), and end-to-end latency. The simulation results show that the B92-based quantum cryptography approach significantly improves throughput efficiency by minimizing key negotiation time while maintaining robust security. This study highlights the effectiveness of integrating quantum cryptography in CPS for building scalable, future-proof, and secure communication systems, ensuring data integrity and privacy against emerging quantum computing threats. © 2025 Elsevier B.V., All rights reserved.